Differences in the water quality can affect the water infiltration process of layered soil. Four kinds of water, deionized water, natural water, natural precipitation and tap water were used to act on three soil configurations (homogeneous loess soil, loess soil with gravel and sand with loess soil), and the influences of these four kinds of water on the infiltration characteristics of the layered soil structures were studied. The results showed that the infiltration descending time order of these four kinds of water in the three soil configurations was: deionized water, natural water, tap water, and natural precipitation. The changing trends of cumulative infiltration amount in the four kinds of water qualities were basically the same, and the descending order of cumulative infiltration amount was: natural water, tap water, deionized water, natural precipitation; sand with loess soil, loess soil with gravel, and homogeneous loess soil. The ascending sort order of advancing distances of wetting front in the same period was: homogeneous loess soil, loess soil with gravel, and sand with loess soil. The influence degree of water quality on infiltration rate, cumulative infiltration amount and the wetting front’s advancing distance of layered soil was determined by the layered combination mode of the soil.